Pseudoexfoliation syndrome (PEXS) may go along with capsular bag shrinkage and luxation. In the present study, we focus on an association of isoforms of TGF-beta with capsular bag luxation. Aqueous humor was collected intraoperatively from 20 healthy controls and from 73 otherwise healthy patients with PEXS [PEXS without complications (PEX, n = 33), late PEXS with glaucoma (PEXG, n = 30) and with IOL and capsular bag luxation (PEXL, n = 10)]. The concentrations of TGF-beta 1, TGF-beta 2 and TGF-beta 3 were compared using the Bio-PlexA (R) multiplex beads system based on the non-parametric Kruskal-Wallis H test (p < 0.01). Concentrations of TGF-beta 1, TGF-beta 2 and TGF-beta 3 were higher in the sub-groups PEX and PEXG than in controls (TGF-beta 1; p = 0.009 and 0.0005; TGF-beta 2; p = 0.002 and 0.005 and TGF-beta 3; 0.0005 and 0.0005; respectively), whereas for TGF beta 2, no significant difference between controls and PEXL was revealed (p = 1.0). TGF-beta 2 concentrations were elevated in a similar degree in early PEX and PEXG, but not in PEXL compared to controls (p = 0.002). The concentrations of of TGF-beta 1 and TGF-beta 3 increased in parallel with the progression of disease. The levels of TGF-beta 3, however, did not attain pathophysiological levels (> 100 pg/ml) in any group. A stage-dependent increase in the concentrations of TGF-beta 1 and TGF-beta 3, but not of TGF-beta 2, accords to the shrinkage of the capsular bag. This could increase the tension on the zonular fibers and contribute to luxation of the capsular bag.